An annotated catalogue of salivary gland transcripts in the adult female mosquito, Ædes ægypti*

Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comParative analyses. In comParative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

Results

The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in s of abundance and length and most contain repeat motifs based on A and T nucleotides.

Conclusion

SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.     

Analysis of signaling pathways in 90 cancer cell lines by protein lysate array

Multiple signal transduction pathways play a crucial role in cancer development, progression, and response to different therapies. An important issue is whether common signal transduction pathways are ubiquitously altered in all cancer types and some unique pathways are involved in different cancer types. Another important issue is whether and how transduction signaling molecules are heterogeneously expressed and activated in different cancer cells within and between cancer cell types. METHODS: To gain insight into these issues, we assembled a protein lysate array with 90 different cell lines of 12 different cell types. Each sample is diluted 2-fold six times, and samples from the dilution series were printed three times on the array. We then measured the expression levels and phosphorylation status of 52 different signaling proteins with specific antibodies and carried out statistical hierarchical clustering analysis. RESULTS: The most significant finding based on the cluster analysis was that the cell lines did not group based on tumor types, suggesting that the signaling pathways studied were commonly activated in most of the tumor types cultured in vitro. As expected, related proteins associated with specific signaling pathways clustered together, and analysis of the 30 most differentially expressed proteins revealed the PI3-K signaling pathway was upregulated in several different tumor types and the VEGF-angiogenesis pathway was downregulated in hematopoetic cancers. Another important observation, with clinical implications was that EGFR was the most heterogeneous among all the cell lines. We also observed signaling pathways unique to specific types of cancers such as the inverse relationship between p16ink and Rb, and the EGFR mediated pathway activation characteristic of pancreatic cancers. CONCLUSIONS: Using reverse phase lysate array analysis in this study, we were able to determine potential relationships and signaling pathways, both common and unique, to different types of cancer using cell lines in vitro. This data could be utilized for mining information related to an individual cancer of interest and combined with morphological and genomic profiles would help in creating a combination of expression markers and/or functional signaling maps for specific cancer diagnosis and therapy.     

Ploidy mosaics: does endopolyploidy in explants affect the cytogenetic stability of orchids regenerated from PLBs?

The induction and regeneration of protocorm-like bodies (PLBs) is a morphogenetic pathway widely used for orchid micropropagation. As endopolyploidy, i.e., the coexistence of cells with different ploidy levels, is a common feature in orchid tissues, a natural question arises when using somatic tissues as explants for orchid micropropagation: does endopolyploidy in explants affect the cytogenetic stability of regenerated plantlets? To answer this question, Epidendrum fulgens was used as a model plant, and flow cytometry was used to analyze endopolyploidy in pollinia, petals, labella, leaf bases, leaf tips, root tips, and protocorm bases and apices, which were subsequently used as explants for PLB induction and plant regeneration. Ploidy screenings showed contrasting ploidy patterns in samples, endopolyploidy being detected in all tissues, with C-values ranging from 1 to 16C. Protocorm bases and root tips presented the highest proportion of endopolyploidy, while petals and protocorm apices showed the lowest proportion. Flower parts exhibited high oxidation for PLB induction and pollinia failed to produce PLB or callus. The highest induction rate occurred at 10 µM TDZ, with 92%, 22%, and 0.92% for protocorm bases, leaves, and root tips, respectively. Plantlets were more easily regenerated from PLBs induced from protocorm bases than from leaves and roots. Doubled ploidy levels were registered in a proportion of 11% and 33% for PLB-regenerated plantlets obtained from protocorm bases and leaf bases, respectively, which was not directly associated with the proportion of endopolyploid cells or cycle value of explants.

     

Biocontrol evaluation of extracts and a major component,clusianone, from Clusia fluminensis Planch. & Triana against Aedes aegypti

Studies evaluated the effects of hexanic extracts from the fruits and flowers ofClusia fluminensis and the main component of the flower extract, a purified benzophenone (clusianone), against Aedes aegypti. The treatment of larvae with the crude fruit or flower extracts from C. fluminensis did not affect the survival ofAe. aegypti (50 mg/L), however, the flower extracts significantly delayed development of Ae. aegypti. In contrast, the clusianone (50 mg/L) isolate from the flower extract, representing 54.85% of this sample composition, showed a highly significant inhibition of survival, killing 93.3% of the larvae and completely blocking development of Ae. aegypti. The results showed, for the first time, high activity of clusianone against Ae. aegypti that both killed and inhibited mosquito development. Therefore, clusianone has potential for development as a biopesticide for controlling insect vectors of tropical diseases. Future work will elucidate the mode of action of clusianone isolated from C. fluminensis.     

Patient's cells colonize the biofilm of Tenckhoff catheters used in peritoneal dialysis

Peritoneal dialysis (PD) is a renal substitutive therapy based on the infusion of a dialysate in the peritoneum, which induces through an osmotic gradient the ultrafiltration of water and the clearance of blood stream impurities by the peritoneal membrane. The colonization of Tenckhoff catheters (TCs) used in PD by pathogenic microorganisms can lead to peritonitis, and probably catheter removal. Here, optical microscopy and scanning electron microscopy were applied to study biofilm formation in 11 TCs. Biofilms varied in their morphology and thickness. Short-term catheters (6 months) presented thinner deposits (3 μm) with granular or flat morphologies, either on the intraluminal or external surfaces. Bacterial colonies were found on catheters from infected patients. A tendency was observed for long-term catheters (6-8 years) to present thicker biofilms (30-35 μm). Surprisingly, patients' cells colonized the deep layers of the thicker biofilms, forming a complex multicelullar community. It was concluded that the presence of a biofilm is not necessarily related with peritonitis, and biofilm features may correlate to the therapy time.     

Evaluating the life‐history trade‐off between dispersal capability and reproduction in wing dimorphic insects: a meta‐analysis

A life‐history trade‐off exists between flight capability and reproduction in many wing dimorphic insects: a long‐winged morph is flight‐capable at the expense of reproduction, while a short‐winged morph cannot fly, is less mobile, but has greater reproductive output. Using meta‐analyses, I investigated specific questions regarding this trade‐off. The trade‐off in females was expressed primarily as a later onset of egg production and lower fecundity in long‐winged females relative to short‐winged females. Although considerably less work has been done with males, the trade‐off exists for males among traits primarily related to mate acquisition. The trade‐off can potentially be mitigated in males, as long‐winged individuals possess an advantage in traits that can offset the costs of flight capability such as a shorter development time. The strength and direction of trends differed significantly among insect orders, and there was a relationship between the strength and direction of trends with the relative flight capabilities between the morphs. I discuss how the trade‐off might be both under‐ and overestimated in the literature, especially in light of work that has examined two relevant aspects of wing dimorphic species: (1) the effect of flight‐muscle histolysis on reproductive investment; and (2) the performance of actual flight by flight‐capable individuals.     

Phosphorylation of histone H3S10 in animal chromosomes: is there a uniform pattern?

Phosphorylation of serine 10 in histone H3 (H3S10ph) has been extensively analyzed and appears to be a conserved chromatin change associated with chromosome condensation in different eukaryotic organisms. In this work, we report the distribution of H3S10ph during meiosis in monocentric and holokinetic chromosomes of 6 insect species and in mitotic chromosomes of 7 mammalian species, aiming to investigate the labeling patterns in phylogenetically distant groups. The results indicated a very similar phosphorylation timing and distribution pattern among insects. The sex chromosomes of insects analyzed were always undercondensed and hypophosphorylated. Similarly, the micro chromosomes of the bug Pachylis aff pharaonis were also undercondensed and hypophosphorylated. Holokinetic chromosomes of bugs and monocentric chromosomes of grasshoppers and beetles displayed identical phosphorylation pattern in spite of the difference in the centromere type. Among mammals, a uniform chromosome phosphorylation was observed in marsupials, whereas bat chromosomes displayed a longitudinal banding pattern. These data indicate that, in general, the intensity of H3S10 phosphorylation in animal chromosomes is variable among the distinct chromosome types and associated with the degree of chromatin condensation at metaphase, but it may vary between different groups of animals.     

Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification

The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM), and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE). Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH) analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be 'missed', only 30% of non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ～50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ～20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used to increase power and compensate for increased error rates.